Peter and Greg;

> > 2. Determine if a BAM file is sorted before it is introduced into the
> > Galaxy environment so that it will only be sorted if necessary.  We have
> > a very simple test for this in the Bam class's _is_coordinate_sorted(0
> > method in ~/lib/galaxy/datatypes/binary.py, but this method obviously
> > needs improvements.  The improved implementation is a bit non-trivial,
> > but it is high priority, so should be completed soon.  In the meantime,
> > Bam files cannot be uploaded to a data library using the combinations
> > of options described in 1 above if they do not pass the current simple,
> > rigid test in the Bam class's method.

> I was thinking about this over the weekend, and perhaps you could
> assume (for the special case of a library import where the file is being
> linked to) that if the BAI index file already exists then the BAM file
> should be sorted already. i.e. Use both the BAM and BAI files as
> provided.

I added in that initial sorted test and agree that it is imperfect.
Several tools sort the files but do not set the SO: header since
it's not required by the spec. We recently had a discussion about
this:

http://biostar.stackexchange.com/questions/5273/is-my-bam-file-sorted

I believe the new 0.1.13 samtools has the fixes Heng mentioned in
the comments thread so a good process to check for sorting is to do
'samtools index your.bam' and check the error code. It will complain
for non-sorted files. The only disadvantage is that you need a new 
samtools for it to work on 100% of cases but that seems like a good
choice moving forward.

Brad
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